Couple of issues I'll highlight with Powtoon.
Support - They always sort in the end, but when you do have issues with items not exporting etc they can be very slow to sort it out.
Web based - When you really push the interface (5 minutes plus, lots of videos and pictures, animations etc) It can bog down and become unresponsive even on massively powerful computers.
Sounds - Powtoon have only just added sound effects and, bizarrely, you can only use the in built ones which are pretty dire. Review collected by and hosted on G2.com.